Multiple sequence alignment - TraesCS5D01G342900
BLAST Results
Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.
qseqid | sseqid | percentage.identical | alignment.length | no.mismatch | no.gap.openings | qstart | qend | sstart | send | evalue | bitscore | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | TraesCS5D01G342900 | chr5D | 100.000 | 2423 | 0 | 0 | 1 | 2423 | 431126274 | 431128696 | 0.000000e+00 | 4475.0 |
1 | TraesCS5D01G342900 | chr5D | 92.208 | 154 | 7 | 2 | 1823 | 1976 | 29486605 | 29486457 | 1.890000e-51 | 213.0 |
2 | TraesCS5D01G342900 | chr5D | 95.745 | 47 | 1 | 1 | 1650 | 1696 | 98437169 | 98437214 | 9.290000e-10 | 75.0 |
3 | TraesCS5D01G342900 | chr5D | 81.818 | 88 | 12 | 4 | 707 | 791 | 339070994 | 339071080 | 1.200000e-08 | 71.3 |
4 | TraesCS5D01G342900 | chr5D | 87.273 | 55 | 5 | 1 | 1651 | 1705 | 141214664 | 141214612 | 7.230000e-06 | 62.1 |
5 | TraesCS5D01G342900 | chr5D | 97.222 | 36 | 0 | 1 | 708 | 742 | 414770747 | 414770712 | 2.600000e-05 | 60.2 |
6 | TraesCS5D01G342900 | chr5B | 91.133 | 1703 | 99 | 20 | 171 | 1828 | 520551089 | 520552784 | 0.000000e+00 | 2261.0 |
7 | TraesCS5D01G342900 | chr5B | 93.548 | 186 | 11 | 1 | 1 | 186 | 520550512 | 520550696 | 2.370000e-70 | 276.0 |
8 | TraesCS5D01G342900 | chr5B | 90.452 | 199 | 18 | 1 | 2225 | 2422 | 520553505 | 520553703 | 6.640000e-66 | 261.0 |
9 | TraesCS5D01G342900 | chr5A | 86.634 | 1025 | 86 | 28 | 659 | 1653 | 546385269 | 546386272 | 0.000000e+00 | 1086.0 |
10 | TraesCS5D01G342900 | chr5A | 89.168 | 517 | 29 | 11 | 157 | 661 | 546384722 | 546385223 | 9.520000e-174 | 619.0 |
11 | TraesCS5D01G342900 | chr5A | 96.241 | 133 | 5 | 0 | 411 | 543 | 504869441 | 504869573 | 4.060000e-53 | 219.0 |
12 | TraesCS5D01G342900 | chr5A | 87.755 | 49 | 5 | 1 | 708 | 755 | 546343308 | 546343260 | 3.370000e-04 | 56.5 |
13 | TraesCS5D01G342900 | chrUn | 92.157 | 153 | 10 | 2 | 1825 | 1976 | 334937675 | 334937524 | 5.250000e-52 | 215.0 |
14 | TraesCS5D01G342900 | chr3B | 90.798 | 163 | 11 | 4 | 1816 | 1976 | 57244712 | 57244872 | 5.250000e-52 | 215.0 |
15 | TraesCS5D01G342900 | chr3B | 90.798 | 163 | 11 | 4 | 1816 | 1976 | 57272134 | 57272294 | 5.250000e-52 | 215.0 |
16 | TraesCS5D01G342900 | chr3B | 93.617 | 47 | 1 | 1 | 1650 | 1696 | 431771259 | 431771303 | 4.320000e-08 | 69.4 |
17 | TraesCS5D01G342900 | chr1D | 92.414 | 145 | 9 | 2 | 1825 | 1968 | 269813369 | 269813226 | 3.160000e-49 | 206.0 |
18 | TraesCS5D01G342900 | chr1D | 90.066 | 151 | 11 | 4 | 1825 | 1974 | 124675032 | 124674885 | 2.460000e-45 | 193.0 |
19 | TraesCS5D01G342900 | chr7D | 90.000 | 160 | 9 | 5 | 1816 | 1974 | 530411025 | 530411178 | 1.470000e-47 | 200.0 |
20 | TraesCS5D01G342900 | chr7D | 84.404 | 109 | 13 | 4 | 2255 | 2360 | 629242510 | 629242403 | 1.180000e-18 | 104.0 |
21 | TraesCS5D01G342900 | chr6D | 90.789 | 152 | 11 | 3 | 1825 | 1976 | 329884380 | 329884232 | 1.470000e-47 | 200.0 |
22 | TraesCS5D01G342900 | chr6D | 100.000 | 28 | 0 | 0 | 2129 | 2156 | 467150607 | 467150634 | 4.000000e-03 | 52.8 |
23 | TraesCS5D01G342900 | chr4A | 89.474 | 152 | 12 | 4 | 1825 | 1974 | 433665489 | 433665340 | 3.180000e-44 | 189.0 |
24 | TraesCS5D01G342900 | chr3D | 95.652 | 46 | 1 | 1 | 1651 | 1696 | 450346595 | 450346639 | 3.340000e-09 | 73.1 |
25 | TraesCS5D01G342900 | chr1A | 84.416 | 77 | 9 | 3 | 717 | 791 | 573386371 | 573386446 | 3.340000e-09 | 73.1 |
26 | TraesCS5D01G342900 | chr6A | 83.333 | 84 | 6 | 7 | 717 | 797 | 103672844 | 103672766 | 1.200000e-08 | 71.3 |
27 | TraesCS5D01G342900 | chr1B | 81.818 | 88 | 12 | 4 | 707 | 791 | 395203829 | 395203743 | 1.200000e-08 | 71.3 |
28 | TraesCS5D01G342900 | chr6B | 93.617 | 47 | 1 | 1 | 1647 | 1693 | 39949606 | 39949650 | 4.320000e-08 | 69.4 |
29 | TraesCS5D01G342900 | chr2B | 93.617 | 47 | 1 | 1 | 1650 | 1696 | 457550629 | 457550585 | 4.320000e-08 | 69.4 |
30 | TraesCS5D01G342900 | chr7A | 83.117 | 77 | 10 | 3 | 717 | 791 | 664772675 | 664772600 | 1.550000e-07 | 67.6 |
31 | TraesCS5D01G342900 | chr4D | 93.478 | 46 | 1 | 1 | 1648 | 1693 | 54763618 | 54763661 | 1.550000e-07 | 67.6 |
32 | TraesCS5D01G342900 | chr7B | 87.500 | 56 | 5 | 1 | 1650 | 1705 | 613317926 | 613317873 | 2.010000e-06 | 63.9 |
33 | TraesCS5D01G342900 | chr4B | 96.970 | 33 | 0 | 1 | 2126 | 2157 | 387798866 | 387798834 | 1.000000e-03 | 54.7 |
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.
query | scaffold | start | end | length | rev.comp | avg.bitscore | max.bitscore | avg.percent.identical | query.start | query.end | num_hsp | groupid | homo_length | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | TraesCS5D01G342900 | chr5D | 431126274 | 431128696 | 2422 | False | 4475.000000 | 4475 | 100.000 | 1 | 2423 | 1 | chr5D.!!$F3 | 2422 |
1 | TraesCS5D01G342900 | chr5B | 520550512 | 520553703 | 3191 | False | 932.666667 | 2261 | 91.711 | 1 | 2422 | 3 | chr5B.!!$F1 | 2421 |
2 | TraesCS5D01G342900 | chr5A | 546384722 | 546386272 | 1550 | False | 852.500000 | 1086 | 87.901 | 157 | 1653 | 2 | chr5A.!!$F2 | 1496 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
64 | 65 | 0.370273 | CTTCGGAGTTTGATTCGCCG | 59.63 | 55.0 | 0.0 | 0.0 | 46.42 | 6.46 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2057 | 2717 | 0.182775 | AGGCTCACGGGTGAAAAACT | 59.817 | 50.0 | 2.81 | 0.0 | 39.39 | 2.66 | R |
All possible primersListed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
29 | 30 | 5.469084 | GGGATTAATTAGTTTAGGGTGCGAG | 59.531 | 44.000 | 0.00 | 0.00 | 0.00 | 5.03 |
48 | 49 | 3.364366 | CGAGTGACAGGCATTTTGACTTC | 60.364 | 47.826 | 0.00 | 0.00 | 29.42 | 3.01 |
49 | 50 | 2.549754 | AGTGACAGGCATTTTGACTTCG | 59.450 | 45.455 | 0.00 | 0.00 | 29.42 | 3.79 |
51 | 52 | 2.151202 | GACAGGCATTTTGACTTCGGA | 58.849 | 47.619 | 0.00 | 0.00 | 29.42 | 4.55 |
64 | 65 | 0.370273 | CTTCGGAGTTTGATTCGCCG | 59.630 | 55.000 | 0.00 | 0.00 | 46.42 | 6.46 |
239 | 652 | 1.598132 | GACGATTCTGTCTCGATCGGA | 59.402 | 52.381 | 16.41 | 8.74 | 39.38 | 4.55 |
288 | 701 | 3.636043 | ACAAAGTGGACGCACGCG | 61.636 | 61.111 | 10.36 | 10.36 | 46.03 | 6.01 |
291 | 704 | 2.380410 | AAAGTGGACGCACGCGATC | 61.380 | 57.895 | 19.66 | 11.41 | 42.83 | 3.69 |
313 | 726 | 4.133078 | CAATTCCAACTGCCTATCTCTCC | 58.867 | 47.826 | 0.00 | 0.00 | 0.00 | 3.71 |
475 | 918 | 1.213094 | ACGACGCGGAACAAAGACTG | 61.213 | 55.000 | 12.47 | 0.00 | 0.00 | 3.51 |
685 | 1177 | 6.617371 | AGATATGTACATTTGTCCTTCCTCCT | 59.383 | 38.462 | 14.77 | 0.00 | 0.00 | 3.69 |
688 | 1180 | 5.701224 | TGTACATTTGTCCTTCCTCCTTTT | 58.299 | 37.500 | 0.00 | 0.00 | 0.00 | 2.27 |
779 | 1271 | 8.854979 | TTCATTCATGCAATAAGTAATTTCGG | 57.145 | 30.769 | 0.00 | 0.00 | 0.00 | 4.30 |
785 | 1280 | 4.569162 | TGCAATAAGTAATTTCGGACGGAG | 59.431 | 41.667 | 0.00 | 0.00 | 0.00 | 4.63 |
786 | 1281 | 4.025145 | GCAATAAGTAATTTCGGACGGAGG | 60.025 | 45.833 | 0.00 | 0.00 | 0.00 | 4.30 |
787 | 1282 | 2.685850 | AAGTAATTTCGGACGGAGGG | 57.314 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
799 | 1294 | 2.228925 | GACGGAGGGGTAGTAGATGAC | 58.771 | 57.143 | 0.00 | 0.00 | 0.00 | 3.06 |
883 | 1381 | 5.079689 | TCTGTTGACGCCATGAATAACTA | 57.920 | 39.130 | 0.00 | 0.00 | 0.00 | 2.24 |
884 | 1382 | 5.670485 | TCTGTTGACGCCATGAATAACTAT | 58.330 | 37.500 | 0.00 | 0.00 | 0.00 | 2.12 |
918 | 1416 | 7.009907 | GCTTTTTCTGACATTTTATCATGCTCC | 59.990 | 37.037 | 0.00 | 0.00 | 0.00 | 4.70 |
938 | 1436 | 2.422803 | CCAGAGAACCAAAACAGTCCCA | 60.423 | 50.000 | 0.00 | 0.00 | 0.00 | 4.37 |
962 | 1460 | 0.788391 | GGTCATTCGGTCAACACGAC | 59.212 | 55.000 | 0.00 | 0.00 | 44.57 | 4.34 |
1030 | 1529 | 1.666599 | CCAATTGTCACCGTACGTCGA | 60.667 | 52.381 | 15.21 | 7.15 | 42.86 | 4.20 |
1035 | 1534 | 4.388080 | CACCGTACGTCGACCGCA | 62.388 | 66.667 | 15.21 | 0.00 | 42.86 | 5.69 |
1093 | 1592 | 0.604511 | CCTACAAAAACCCGGCGACT | 60.605 | 55.000 | 9.30 | 0.00 | 0.00 | 4.18 |
1460 | 1983 | 2.672307 | TGCATGGCATCGCACACA | 60.672 | 55.556 | 16.90 | 0.00 | 31.71 | 3.72 |
1474 | 1997 | 1.798223 | GCACACAACTCAAGATACGCA | 59.202 | 47.619 | 0.00 | 0.00 | 0.00 | 5.24 |
1481 | 2004 | 1.733912 | ACTCAAGATACGCACGTACGA | 59.266 | 47.619 | 24.41 | 0.00 | 36.70 | 3.43 |
1505 | 2029 | 1.089481 | TCATCGGAGGAAACATGCGC | 61.089 | 55.000 | 0.00 | 0.00 | 0.00 | 6.09 |
1552 | 2082 | 4.090034 | CGTTCGTGACTAGCTAGTTCTTC | 58.910 | 47.826 | 26.71 | 14.64 | 36.50 | 2.87 |
1568 | 2098 | 8.454106 | GCTAGTTCTTCTTGAATTCATTTGCTA | 58.546 | 33.333 | 9.40 | 5.46 | 36.99 | 3.49 |
1684 | 2214 | 7.389053 | AGTTCTTGATTGTTTTTCGAGATAGCT | 59.611 | 33.333 | 0.00 | 0.00 | 34.39 | 3.32 |
1713 | 2243 | 6.291743 | CGCTTATTTCACGCGGTAAGTTTATA | 60.292 | 38.462 | 12.47 | 0.00 | 42.88 | 0.98 |
1780 | 2310 | 3.307108 | TGTGGGTGCCGATCGTCA | 61.307 | 61.111 | 15.09 | 4.04 | 0.00 | 4.35 |
1785 | 2315 | 0.946221 | GGGTGCCGATCGTCATCATC | 60.946 | 60.000 | 11.95 | 5.34 | 0.00 | 2.92 |
1823 | 2353 | 8.589701 | TTTTCGCTGTATCTCCTATATATGGA | 57.410 | 34.615 | 0.00 | 1.27 | 0.00 | 3.41 |
1824 | 2354 | 7.569639 | TTCGCTGTATCTCCTATATATGGAC | 57.430 | 40.000 | 0.00 | 0.00 | 0.00 | 4.02 |
1825 | 2355 | 6.659824 | TCGCTGTATCTCCTATATATGGACA | 58.340 | 40.000 | 0.00 | 0.00 | 0.00 | 4.02 |
1827 | 2357 | 7.283354 | TCGCTGTATCTCCTATATATGGACAAG | 59.717 | 40.741 | 0.00 | 0.00 | 0.00 | 3.16 |
1828 | 2358 | 7.283354 | CGCTGTATCTCCTATATATGGACAAGA | 59.717 | 40.741 | 0.00 | 0.00 | 0.00 | 3.02 |
1829 | 2359 | 9.142014 | GCTGTATCTCCTATATATGGACAAGAT | 57.858 | 37.037 | 0.00 | 5.93 | 0.00 | 2.40 |
1834 | 2364 | 8.815565 | TCTCCTATATATGGACAAGATGAGTC | 57.184 | 38.462 | 0.00 | 0.00 | 35.29 | 3.36 |
1835 | 2365 | 8.619281 | TCTCCTATATATGGACAAGATGAGTCT | 58.381 | 37.037 | 0.00 | 0.00 | 36.29 | 3.24 |
1841 | 2371 | 5.736951 | ATGGACAAGATGAGTCTATAGCC | 57.263 | 43.478 | 0.00 | 0.00 | 35.74 | 3.93 |
1842 | 2372 | 4.809193 | TGGACAAGATGAGTCTATAGCCT | 58.191 | 43.478 | 0.00 | 0.00 | 36.29 | 4.58 |
1843 | 2373 | 5.953571 | TGGACAAGATGAGTCTATAGCCTA | 58.046 | 41.667 | 0.00 | 0.00 | 36.29 | 3.93 |
1844 | 2374 | 6.373759 | TGGACAAGATGAGTCTATAGCCTAA | 58.626 | 40.000 | 0.00 | 0.00 | 36.29 | 2.69 |
1845 | 2375 | 7.013220 | TGGACAAGATGAGTCTATAGCCTAAT | 58.987 | 38.462 | 0.00 | 0.00 | 36.29 | 1.73 |
1846 | 2376 | 8.170730 | TGGACAAGATGAGTCTATAGCCTAATA | 58.829 | 37.037 | 0.00 | 0.00 | 36.29 | 0.98 |
1863 | 2393 | 8.807948 | AGCCTAATAAATGAAGTGTTACATGT | 57.192 | 30.769 | 2.69 | 2.69 | 0.00 | 3.21 |
1864 | 2394 | 9.243105 | AGCCTAATAAATGAAGTGTTACATGTT | 57.757 | 29.630 | 2.30 | 0.00 | 0.00 | 2.71 |
1871 | 2401 | 5.994887 | TGAAGTGTTACATGTTACCACAC | 57.005 | 39.130 | 12.16 | 14.80 | 38.43 | 3.82 |
1872 | 2402 | 5.429130 | TGAAGTGTTACATGTTACCACACA | 58.571 | 37.500 | 22.19 | 17.31 | 40.23 | 3.72 |
1876 | 2406 | 7.609760 | AGTGTTACATGTTACCACACATATG | 57.390 | 36.000 | 22.19 | 0.00 | 40.23 | 1.78 |
1878 | 2408 | 7.663905 | AGTGTTACATGTTACCACACATATGTT | 59.336 | 33.333 | 22.19 | 0.00 | 40.23 | 2.71 |
1879 | 2409 | 8.937884 | GTGTTACATGTTACCACACATATGTTA | 58.062 | 33.333 | 12.16 | 0.00 | 36.72 | 2.41 |
1880 | 2410 | 8.937884 | TGTTACATGTTACCACACATATGTTAC | 58.062 | 33.333 | 12.16 | 0.00 | 36.72 | 2.50 |
1882 | 2412 | 7.843490 | ACATGTTACCACACATATGTTACTC | 57.157 | 36.000 | 5.37 | 0.00 | 36.72 | 2.59 |
1883 | 2413 | 6.821665 | ACATGTTACCACACATATGTTACTCC | 59.178 | 38.462 | 5.37 | 0.00 | 36.72 | 3.85 |
1885 | 2415 | 3.926058 | ACCACACATATGTTACTCCCC | 57.074 | 47.619 | 5.37 | 0.00 | 36.72 | 4.81 |
1886 | 2416 | 3.186283 | ACCACACATATGTTACTCCCCA | 58.814 | 45.455 | 5.37 | 0.00 | 36.72 | 4.96 |
1887 | 2417 | 3.054655 | ACCACACATATGTTACTCCCCAC | 60.055 | 47.826 | 5.37 | 0.00 | 36.72 | 4.61 |
1888 | 2418 | 3.199946 | CCACACATATGTTACTCCCCACT | 59.800 | 47.826 | 5.37 | 0.00 | 36.72 | 4.00 |
1889 | 2419 | 4.407621 | CCACACATATGTTACTCCCCACTA | 59.592 | 45.833 | 5.37 | 0.00 | 36.72 | 2.74 |
1890 | 2420 | 5.071788 | CCACACATATGTTACTCCCCACTAT | 59.928 | 44.000 | 5.37 | 0.00 | 36.72 | 2.12 |
1891 | 2421 | 6.269077 | CCACACATATGTTACTCCCCACTATA | 59.731 | 42.308 | 5.37 | 0.00 | 36.72 | 1.31 |
1892 | 2422 | 7.378966 | CACACATATGTTACTCCCCACTATAG | 58.621 | 42.308 | 5.37 | 0.00 | 36.72 | 1.31 |
1893 | 2423 | 7.232737 | CACACATATGTTACTCCCCACTATAGA | 59.767 | 40.741 | 5.37 | 0.00 | 36.72 | 1.98 |
1895 | 2425 | 6.954684 | ACATATGTTACTCCCCACTATAGAGG | 59.045 | 42.308 | 6.78 | 8.10 | 31.70 | 3.69 |
1896 | 2426 | 4.894252 | TGTTACTCCCCACTATAGAGGT | 57.106 | 45.455 | 14.29 | 0.00 | 31.70 | 3.85 |
1897 | 2427 | 5.999987 | TGTTACTCCCCACTATAGAGGTA | 57.000 | 43.478 | 14.29 | 2.62 | 31.70 | 3.08 |
1898 | 2428 | 5.950023 | TGTTACTCCCCACTATAGAGGTAG | 58.050 | 45.833 | 14.29 | 12.87 | 31.70 | 3.18 |
1900 | 2430 | 6.621098 | TGTTACTCCCCACTATAGAGGTAGTA | 59.379 | 42.308 | 17.42 | 17.42 | 33.29 | 1.82 |
1901 | 2431 | 7.129349 | TGTTACTCCCCACTATAGAGGTAGTAA | 59.871 | 40.741 | 23.15 | 23.15 | 33.91 | 2.24 |
1902 | 2432 | 5.951204 | ACTCCCCACTATAGAGGTAGTAAC | 58.049 | 45.833 | 14.29 | 0.00 | 33.29 | 2.50 |
1904 | 2434 | 6.104392 | ACTCCCCACTATAGAGGTAGTAACAT | 59.896 | 42.308 | 14.29 | 0.00 | 33.29 | 2.71 |
1905 | 2435 | 7.296628 | ACTCCCCACTATAGAGGTAGTAACATA | 59.703 | 40.741 | 14.29 | 0.00 | 33.29 | 2.29 |
1906 | 2436 | 7.696981 | TCCCCACTATAGAGGTAGTAACATAG | 58.303 | 42.308 | 14.29 | 0.00 | 33.29 | 2.23 |
1907 | 2437 | 7.518653 | TCCCCACTATAGAGGTAGTAACATAGA | 59.481 | 40.741 | 14.29 | 0.00 | 33.29 | 1.98 |
1908 | 2438 | 7.830201 | CCCCACTATAGAGGTAGTAACATAGAG | 59.170 | 44.444 | 14.29 | 0.00 | 33.29 | 2.43 |
1919 | 2449 | 9.917887 | AGGTAGTAACATAGAGTAGTAACATGT | 57.082 | 33.333 | 0.00 | 0.00 | 0.00 | 3.21 |
1978 | 2638 | 5.810080 | ACCCATTATGGCTAGTCTTACTC | 57.190 | 43.478 | 5.57 | 0.00 | 35.79 | 2.59 |
2005 | 2665 | 6.650807 | CACACAATGTCTACTTTAGTGTGGAT | 59.349 | 38.462 | 20.92 | 0.41 | 46.82 | 3.41 |
2006 | 2666 | 6.874134 | ACACAATGTCTACTTTAGTGTGGATC | 59.126 | 38.462 | 8.56 | 0.00 | 37.35 | 3.36 |
2034 | 2694 | 3.731547 | TGGCCTGACCAGATGGAG | 58.268 | 61.111 | 3.32 | 0.00 | 46.36 | 3.86 |
2035 | 2695 | 1.997311 | TGGCCTGACCAGATGGAGG | 60.997 | 63.158 | 3.32 | 4.04 | 46.36 | 4.30 |
2036 | 2696 | 2.191641 | GCCTGACCAGATGGAGGC | 59.808 | 66.667 | 14.00 | 14.00 | 44.63 | 4.70 |
2039 | 2699 | 0.107312 | CCTGACCAGATGGAGGCTTG | 60.107 | 60.000 | 5.72 | 0.00 | 38.94 | 4.01 |
2065 | 2725 | 1.412343 | GGCTTTGGCTCCAGTTTTTCA | 59.588 | 47.619 | 0.00 | 0.00 | 38.73 | 2.69 |
2066 | 2726 | 2.473816 | GCTTTGGCTCCAGTTTTTCAC | 58.526 | 47.619 | 0.00 | 0.00 | 35.22 | 3.18 |
2074 | 2734 | 0.310854 | CCAGTTTTTCACCCGTGAGC | 59.689 | 55.000 | 0.00 | 0.00 | 41.13 | 4.26 |
2103 | 2763 | 5.393124 | CCGAAAACCCGAATACTTAAAACC | 58.607 | 41.667 | 0.00 | 0.00 | 0.00 | 3.27 |
2127 | 2787 | 5.981088 | ATGACTTGGTGAAAATATGTGCA | 57.019 | 34.783 | 0.00 | 0.00 | 0.00 | 4.57 |
2139 | 2799 | 0.179048 | TATGTGCATTGCTCCCTCCG | 60.179 | 55.000 | 10.49 | 0.00 | 0.00 | 4.63 |
2154 | 2814 | 3.581332 | TCCCTCCGTCTCAAAATAAGTGT | 59.419 | 43.478 | 0.00 | 0.00 | 0.00 | 3.55 |
2236 | 3099 | 9.823647 | CCTATAACTTCATTCATACTCACAACT | 57.176 | 33.333 | 0.00 | 0.00 | 0.00 | 3.16 |
2278 | 3141 | 7.945033 | TTTGAACCATGCTTCAAGAAATTAC | 57.055 | 32.000 | 14.24 | 0.00 | 40.42 | 1.89 |
2298 | 3161 | 7.907214 | ATTACAAACAACTCCTACAGCTAAG | 57.093 | 36.000 | 0.00 | 0.00 | 0.00 | 2.18 |
2328 | 3192 | 6.894103 | ACAATAAATCTCTTGGAGGCATCTTT | 59.106 | 34.615 | 0.00 | 0.00 | 0.00 | 2.52 |
2334 | 3198 | 2.569853 | TCTTGGAGGCATCTTTTCCGTA | 59.430 | 45.455 | 0.00 | 0.00 | 33.60 | 4.02 |
2343 | 3207 | 4.272748 | GGCATCTTTTCCGTAGTATCAACC | 59.727 | 45.833 | 0.00 | 0.00 | 0.00 | 3.77 |
2354 | 3218 | 5.220662 | CCGTAGTATCAACCTTTGCAAGATG | 60.221 | 44.000 | 0.00 | 0.00 | 0.00 | 2.90 |
2359 | 3223 | 8.579850 | AGTATCAACCTTTGCAAGATGAAATA | 57.420 | 30.769 | 0.00 | 0.00 | 31.25 | 1.40 |
2372 | 3236 | 7.982371 | CAAGATGAAATATTGCCAAGACTTC | 57.018 | 36.000 | 0.00 | 0.00 | 38.83 | 3.01 |
2385 | 3249 | 4.378459 | GCCAAGACTTCAACAAATAGACCG | 60.378 | 45.833 | 0.00 | 0.00 | 0.00 | 4.79 |
2388 | 3252 | 4.385825 | AGACTTCAACAAATAGACCGCAA | 58.614 | 39.130 | 0.00 | 0.00 | 0.00 | 4.85 |
2391 | 3255 | 5.699839 | ACTTCAACAAATAGACCGCAATTC | 58.300 | 37.500 | 0.00 | 0.00 | 0.00 | 2.17 |
2397 | 3261 | 2.225068 | ATAGACCGCAATTCGACTGG | 57.775 | 50.000 | 0.00 | 0.00 | 41.67 | 4.00 |
2412 | 3276 | 0.663688 | ACTGGAGTAGCGATACTGCG | 59.336 | 55.000 | 24.20 | 20.41 | 40.66 | 5.18 |
2422 | 3286 | 1.457738 | CGATACTGCGACTCGTTCAG | 58.542 | 55.000 | 0.00 | 2.68 | 0.00 | 3.02 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
4 | 5 | 4.212636 | CGCACCCTAAACTAATTAATCCCG | 59.787 | 45.833 | 0.00 | 0.00 | 0.00 | 5.14 |
11 | 12 | 4.251268 | GTCACTCGCACCCTAAACTAATT | 58.749 | 43.478 | 0.00 | 0.00 | 0.00 | 1.40 |
29 | 30 | 2.350772 | CCGAAGTCAAAATGCCTGTCAC | 60.351 | 50.000 | 0.00 | 0.00 | 0.00 | 3.67 |
48 | 49 | 0.736325 | ACTCGGCGAATCAAACTCCG | 60.736 | 55.000 | 12.13 | 0.00 | 41.30 | 4.63 |
49 | 50 | 0.721718 | CACTCGGCGAATCAAACTCC | 59.278 | 55.000 | 12.13 | 0.00 | 0.00 | 3.85 |
51 | 52 | 2.162716 | GCACTCGGCGAATCAAACT | 58.837 | 52.632 | 12.13 | 0.00 | 0.00 | 2.66 |
64 | 65 | 3.503363 | GCATCGCCACCTGCACTC | 61.503 | 66.667 | 0.00 | 0.00 | 41.33 | 3.51 |
239 | 652 | 1.517832 | CGAAATCGCCTCACCCTCT | 59.482 | 57.895 | 0.00 | 0.00 | 0.00 | 3.69 |
288 | 701 | 5.619220 | AGAGATAGGCAGTTGGAATTGATC | 58.381 | 41.667 | 0.00 | 0.00 | 0.00 | 2.92 |
291 | 704 | 4.133078 | GGAGAGATAGGCAGTTGGAATTG | 58.867 | 47.826 | 0.00 | 0.00 | 0.00 | 2.32 |
313 | 726 | 3.875838 | TTTTTGACCAAATCGCGGG | 57.124 | 47.368 | 6.13 | 0.89 | 0.00 | 6.13 |
419 | 841 | 2.612567 | TTGGGCGACGACAATGTGC | 61.613 | 57.895 | 1.63 | 0.00 | 0.00 | 4.57 |
420 | 842 | 1.206578 | GTTGGGCGACGACAATGTG | 59.793 | 57.895 | 1.63 | 0.00 | 33.39 | 3.21 |
421 | 843 | 1.227704 | TGTTGGGCGACGACAATGT | 60.228 | 52.632 | 1.63 | 0.00 | 40.53 | 2.71 |
475 | 918 | 2.484889 | GGTGAGCTCCCGAATTATGTC | 58.515 | 52.381 | 12.15 | 0.00 | 0.00 | 3.06 |
593 | 1036 | 6.287589 | AGAGTAACCGATTCAAGAGTTGAT | 57.712 | 37.500 | 0.00 | 0.00 | 39.84 | 2.57 |
669 | 1161 | 5.789643 | TCAAAAAGGAGGAAGGACAAATG | 57.210 | 39.130 | 0.00 | 0.00 | 0.00 | 2.32 |
676 | 1168 | 9.243105 | TGATAAGTAATTCAAAAAGGAGGAAGG | 57.757 | 33.333 | 0.00 | 0.00 | 0.00 | 3.46 |
760 | 1252 | 5.007234 | TCCGTCCGAAATTACTTATTGCATG | 59.993 | 40.000 | 0.00 | 0.00 | 0.00 | 4.06 |
779 | 1271 | 2.158638 | AGTCATCTACTACCCCTCCGTC | 60.159 | 54.545 | 0.00 | 0.00 | 36.36 | 4.79 |
785 | 1280 | 4.820894 | AACAACAGTCATCTACTACCCC | 57.179 | 45.455 | 0.00 | 0.00 | 35.76 | 4.95 |
786 | 1281 | 5.790593 | TGAAACAACAGTCATCTACTACCC | 58.209 | 41.667 | 0.00 | 0.00 | 35.76 | 3.69 |
787 | 1282 | 6.688578 | TCTGAAACAACAGTCATCTACTACC | 58.311 | 40.000 | 0.00 | 0.00 | 35.76 | 3.18 |
799 | 1294 | 6.549912 | TGACATGAAGATCTGAAACAACAG | 57.450 | 37.500 | 0.00 | 0.00 | 39.02 | 3.16 |
883 | 1381 | 8.424274 | AAAATGTCAGAAAAAGCGAGAAAAAT | 57.576 | 26.923 | 0.00 | 0.00 | 0.00 | 1.82 |
884 | 1382 | 7.826260 | AAAATGTCAGAAAAAGCGAGAAAAA | 57.174 | 28.000 | 0.00 | 0.00 | 0.00 | 1.94 |
918 | 1416 | 2.618709 | GTGGGACTGTTTTGGTTCTCTG | 59.381 | 50.000 | 0.00 | 0.00 | 0.00 | 3.35 |
962 | 1460 | 1.012486 | GCGTTACCACTGTTCCTCGG | 61.012 | 60.000 | 0.00 | 0.00 | 0.00 | 4.63 |
1030 | 1529 | 2.042831 | GCCATGAGAGCTTTGCGGT | 61.043 | 57.895 | 0.00 | 0.00 | 0.00 | 5.68 |
1035 | 1534 | 2.439156 | GGCGGCCATGAGAGCTTT | 60.439 | 61.111 | 15.62 | 0.00 | 0.00 | 3.51 |
1096 | 1595 | 2.750888 | GCGATGCTTGGACGGGAAC | 61.751 | 63.158 | 0.00 | 0.00 | 0.00 | 3.62 |
1414 | 1930 | 2.590007 | ATGATCGGCTCAAGCGGC | 60.590 | 61.111 | 4.80 | 0.00 | 43.26 | 6.53 |
1460 | 1983 | 2.160219 | TCGTACGTGCGTATCTTGAGTT | 59.840 | 45.455 | 24.94 | 0.00 | 32.82 | 3.01 |
1505 | 2029 | 2.789917 | GAACAGAGCATGCAGGCG | 59.210 | 61.111 | 21.98 | 6.43 | 39.27 | 5.52 |
1515 | 2039 | 2.724690 | ACGAACGAATGAACGAACAGAG | 59.275 | 45.455 | 0.14 | 0.00 | 37.03 | 3.35 |
1516 | 2040 | 2.469886 | CACGAACGAATGAACGAACAGA | 59.530 | 45.455 | 0.14 | 0.00 | 37.03 | 3.41 |
1552 | 2082 | 9.414295 | TCAAAGACAATAGCAAATGAATTCAAG | 57.586 | 29.630 | 13.09 | 6.87 | 0.00 | 3.02 |
1568 | 2098 | 6.282930 | CACCAGGTTGAAAATCAAAGACAAT | 58.717 | 36.000 | 0.00 | 0.00 | 38.22 | 2.71 |
1582 | 2112 | 2.186160 | CAAGCACGCACCAGGTTGA | 61.186 | 57.895 | 0.00 | 0.00 | 43.77 | 3.18 |
1655 | 2185 | 5.751509 | TCTCGAAAAACAATCAAGAACTCGA | 59.248 | 36.000 | 0.00 | 0.00 | 0.00 | 4.04 |
1665 | 2195 | 5.050972 | CGGGTAGCTATCTCGAAAAACAATC | 60.051 | 44.000 | 3.53 | 0.00 | 0.00 | 2.67 |
1666 | 2196 | 4.809426 | CGGGTAGCTATCTCGAAAAACAAT | 59.191 | 41.667 | 3.53 | 0.00 | 0.00 | 2.71 |
1780 | 2310 | 9.941664 | CAGCGAAAATAATTAACAAGAGATGAT | 57.058 | 29.630 | 0.00 | 0.00 | 0.00 | 2.45 |
1801 | 2331 | 6.659824 | TGTCCATATATAGGAGATACAGCGA | 58.340 | 40.000 | 0.00 | 0.00 | 35.42 | 4.93 |
1815 | 2345 | 9.142014 | GGCTATAGACTCATCTTGTCCATATAT | 57.858 | 37.037 | 3.21 | 0.00 | 36.29 | 0.86 |
1819 | 2349 | 5.401750 | AGGCTATAGACTCATCTTGTCCAT | 58.598 | 41.667 | 0.83 | 0.00 | 36.29 | 3.41 |
1821 | 2351 | 6.902771 | TTAGGCTATAGACTCATCTTGTCC | 57.097 | 41.667 | 12.64 | 0.00 | 36.29 | 4.02 |
1862 | 2392 | 5.121105 | GGGGAGTAACATATGTGTGGTAAC | 58.879 | 45.833 | 9.63 | 1.91 | 38.92 | 2.50 |
1863 | 2393 | 4.783763 | TGGGGAGTAACATATGTGTGGTAA | 59.216 | 41.667 | 9.63 | 0.00 | 38.92 | 2.85 |
1864 | 2394 | 4.162698 | GTGGGGAGTAACATATGTGTGGTA | 59.837 | 45.833 | 9.63 | 0.00 | 38.92 | 3.25 |
1866 | 2396 | 3.199946 | AGTGGGGAGTAACATATGTGTGG | 59.800 | 47.826 | 9.63 | 0.00 | 38.92 | 4.17 |
1867 | 2397 | 4.487714 | AGTGGGGAGTAACATATGTGTG | 57.512 | 45.455 | 9.63 | 0.00 | 38.92 | 3.82 |
1869 | 2399 | 7.093727 | CCTCTATAGTGGGGAGTAACATATGTG | 60.094 | 44.444 | 9.63 | 0.00 | 0.00 | 3.21 |
1871 | 2401 | 6.954684 | ACCTCTATAGTGGGGAGTAACATATG | 59.045 | 42.308 | 21.82 | 0.00 | 33.22 | 1.78 |
1872 | 2402 | 7.117331 | ACCTCTATAGTGGGGAGTAACATAT | 57.883 | 40.000 | 21.82 | 0.00 | 33.22 | 1.78 |
1876 | 2406 | 5.951204 | ACTACCTCTATAGTGGGGAGTAAC | 58.049 | 45.833 | 22.09 | 0.00 | 34.02 | 2.50 |
1878 | 2408 | 6.621098 | TGTTACTACCTCTATAGTGGGGAGTA | 59.379 | 42.308 | 23.32 | 23.32 | 36.09 | 2.59 |
1879 | 2409 | 5.434376 | TGTTACTACCTCTATAGTGGGGAGT | 59.566 | 44.000 | 24.72 | 24.72 | 36.09 | 3.85 |
1880 | 2410 | 5.950023 | TGTTACTACCTCTATAGTGGGGAG | 58.050 | 45.833 | 21.82 | 20.04 | 36.09 | 4.30 |
1882 | 2412 | 7.696981 | TCTATGTTACTACCTCTATAGTGGGG | 58.303 | 42.308 | 21.82 | 16.35 | 36.09 | 4.96 |
1883 | 2413 | 8.384718 | ACTCTATGTTACTACCTCTATAGTGGG | 58.615 | 40.741 | 21.82 | 16.23 | 36.09 | 4.61 |
1893 | 2423 | 9.917887 | ACATGTTACTACTCTATGTTACTACCT | 57.082 | 33.333 | 0.00 | 0.00 | 0.00 | 3.08 |
1957 | 2487 | 5.540337 | TGAGAGTAAGACTAGCCATAATGGG | 59.460 | 44.000 | 0.00 | 0.00 | 38.19 | 4.00 |
1958 | 2488 | 6.040955 | TGTGAGAGTAAGACTAGCCATAATGG | 59.959 | 42.308 | 0.00 | 0.00 | 41.55 | 3.16 |
1959 | 2489 | 6.920758 | GTGTGAGAGTAAGACTAGCCATAATG | 59.079 | 42.308 | 0.00 | 0.00 | 0.00 | 1.90 |
1961 | 2491 | 5.949952 | TGTGTGAGAGTAAGACTAGCCATAA | 59.050 | 40.000 | 0.00 | 0.00 | 0.00 | 1.90 |
1963 | 2493 | 4.344978 | TGTGTGAGAGTAAGACTAGCCAT | 58.655 | 43.478 | 0.00 | 0.00 | 0.00 | 4.40 |
1966 | 2496 | 5.715070 | ACATTGTGTGAGAGTAAGACTAGC | 58.285 | 41.667 | 0.00 | 0.00 | 0.00 | 3.42 |
1967 | 2497 | 7.151999 | AGACATTGTGTGAGAGTAAGACTAG | 57.848 | 40.000 | 0.00 | 0.00 | 0.00 | 2.57 |
1969 | 2499 | 6.717540 | AGTAGACATTGTGTGAGAGTAAGACT | 59.282 | 38.462 | 0.00 | 0.00 | 0.00 | 3.24 |
1970 | 2500 | 6.915349 | AGTAGACATTGTGTGAGAGTAAGAC | 58.085 | 40.000 | 0.00 | 0.00 | 0.00 | 3.01 |
1971 | 2501 | 7.526142 | AAGTAGACATTGTGTGAGAGTAAGA | 57.474 | 36.000 | 0.00 | 0.00 | 0.00 | 2.10 |
2029 | 2689 | 3.801997 | CCCGCTCCAAGCCTCCAT | 61.802 | 66.667 | 0.00 | 0.00 | 38.18 | 3.41 |
2032 | 2692 | 3.927481 | AAAGCCCGCTCCAAGCCTC | 62.927 | 63.158 | 0.00 | 0.00 | 38.18 | 4.70 |
2033 | 2693 | 3.971702 | AAAGCCCGCTCCAAGCCT | 61.972 | 61.111 | 0.00 | 0.00 | 38.18 | 4.58 |
2034 | 2694 | 3.752339 | CAAAGCCCGCTCCAAGCC | 61.752 | 66.667 | 0.00 | 0.00 | 38.18 | 4.35 |
2035 | 2695 | 3.752339 | CCAAAGCCCGCTCCAAGC | 61.752 | 66.667 | 0.00 | 0.00 | 38.02 | 4.01 |
2036 | 2696 | 3.752339 | GCCAAAGCCCGCTCCAAG | 61.752 | 66.667 | 0.00 | 0.00 | 0.00 | 3.61 |
2057 | 2717 | 0.182775 | AGGCTCACGGGTGAAAAACT | 59.817 | 50.000 | 2.81 | 0.00 | 39.39 | 2.66 |
2074 | 2734 | 3.733295 | TATTCGGGTTTTCGGCCCAGG | 62.733 | 57.143 | 0.00 | 0.00 | 46.40 | 4.45 |
2089 | 2749 | 8.388103 | CACCAAGTCATAGGTTTTAAGTATTCG | 58.612 | 37.037 | 0.00 | 0.00 | 35.52 | 3.34 |
2090 | 2750 | 9.444600 | TCACCAAGTCATAGGTTTTAAGTATTC | 57.555 | 33.333 | 0.00 | 0.00 | 35.52 | 1.75 |
2103 | 2763 | 7.087409 | TGCACATATTTTCACCAAGTCATAG | 57.913 | 36.000 | 0.00 | 0.00 | 0.00 | 2.23 |
2123 | 2783 | 2.045926 | ACGGAGGGAGCAATGCAC | 60.046 | 61.111 | 8.35 | 0.00 | 0.00 | 4.57 |
2127 | 2787 | 0.984230 | TTTGAGACGGAGGGAGCAAT | 59.016 | 50.000 | 0.00 | 0.00 | 0.00 | 3.56 |
2200 | 2860 | 9.911788 | ATGAATGAAGTTATAGGTGTTTCTCAT | 57.088 | 29.630 | 0.00 | 0.00 | 0.00 | 2.90 |
2236 | 3099 | 8.811017 | TGGTTCAAAAGGAATGCATCTTTAATA | 58.189 | 29.630 | 12.36 | 1.47 | 37.93 | 0.98 |
2241 | 3104 | 5.484715 | CATGGTTCAAAAGGAATGCATCTT | 58.515 | 37.500 | 0.00 | 0.00 | 37.93 | 2.40 |
2242 | 3105 | 4.622220 | GCATGGTTCAAAAGGAATGCATCT | 60.622 | 41.667 | 0.00 | 0.00 | 38.38 | 2.90 |
2246 | 3109 | 3.323751 | AGCATGGTTCAAAAGGAATGC | 57.676 | 42.857 | 0.00 | 0.00 | 38.64 | 3.56 |
2278 | 3141 | 7.440523 | AATTCTTAGCTGTAGGAGTTGTTTG | 57.559 | 36.000 | 0.00 | 0.00 | 0.00 | 2.93 |
2298 | 3161 | 8.225603 | TGCCTCCAAGAGATTTATTGTAATTC | 57.774 | 34.615 | 0.00 | 0.00 | 0.00 | 2.17 |
2314 | 3178 | 1.826385 | ACGGAAAAGATGCCTCCAAG | 58.174 | 50.000 | 0.00 | 0.00 | 0.00 | 3.61 |
2328 | 3192 | 4.274602 | TGCAAAGGTTGATACTACGGAA | 57.725 | 40.909 | 0.00 | 0.00 | 0.00 | 4.30 |
2334 | 3198 | 6.899393 | TTTCATCTTGCAAAGGTTGATACT | 57.101 | 33.333 | 0.00 | 0.00 | 46.24 | 2.12 |
2343 | 3207 | 6.971527 | TTGGCAATATTTCATCTTGCAAAG | 57.028 | 33.333 | 0.00 | 0.00 | 45.44 | 2.77 |
2354 | 3218 | 7.945033 | TTTGTTGAAGTCTTGGCAATATTTC | 57.055 | 32.000 | 12.10 | 12.10 | 0.00 | 2.17 |
2359 | 3223 | 6.294731 | GGTCTATTTGTTGAAGTCTTGGCAAT | 60.295 | 38.462 | 0.00 | 0.00 | 0.00 | 3.56 |
2372 | 3236 | 4.088648 | GTCGAATTGCGGTCTATTTGTTG | 58.911 | 43.478 | 0.00 | 0.00 | 41.33 | 3.33 |
2385 | 3249 | 0.924090 | CGCTACTCCAGTCGAATTGC | 59.076 | 55.000 | 0.00 | 0.00 | 0.00 | 3.56 |
2388 | 3252 | 3.251245 | CAGTATCGCTACTCCAGTCGAAT | 59.749 | 47.826 | 0.00 | 0.00 | 35.99 | 3.34 |
2391 | 3255 | 1.334239 | GCAGTATCGCTACTCCAGTCG | 60.334 | 57.143 | 0.00 | 0.00 | 35.99 | 4.18 |
2397 | 3261 | 1.397441 | CGAGTCGCAGTATCGCTACTC | 60.397 | 57.143 | 0.00 | 7.34 | 46.07 | 2.59 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.